Project PXD002462

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Biological Dataset Biomedical Dataset
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Human Protein Tyrosine Phosphatase Interaction Network


As the remarkable prevalence of activated protein tyrosine kinases (TKs) as oncoproteins and their mutations being identified in numerous cancers, the control of protein tyrosine phosphorylation has been considered to play a central role in ensuring the homeostasis of cellular physiology and thus, preventing tumorigenesis. Protein tyrosine phosphatases (PTPs) can contribute to this equilibrium of protein tyrosine phosphorylation and thereby antagonize the oncogenic activities of tyrosine kinases, therefore, PTPs are prominently considered to act as tumor suppressors. To achieve a comprehensive understanding of the protein-protein interaction network for this PTP family, we isolated the ~ 70 PTP-associated protein complexes from HEK293T cells and provided a systematically proteomic analysis for this tumor suppressor family.

Sample Processing Protocol

Excised gel bands were cut into approximately 1 mm3 pieces. Gel pieces were then subjected to in-gel trypsin digestion and dried. Samples were reconstituted in 5 µl of HPLC solvent A (2.5% acetonitrile, 0.1% formic acid). A nano-scale reverse-phase HPLC capillary column was created by packing 5 µm C18 spherical silica beads into a fused silica capillary (100 µm inner diameter x ~20 cm length) with a flame-drawn tip. After equilibrating the column each sample was loaded via a Famos autosampler (LC Packings, San Francisco CA) onto the column. A gradient was formed and peptides were eluted with increasing concentrations of solvent B (97.5% acetonitrile, 0.1% formic acid). As peptides eluted they were subjected to electrospray ionization and then entered into an LTQ Velos ion-trap mass spectrometer (ThermoFisher, San Jose, CA). Peptides were detected, isolated, and fragmented to produce a tandem mass spectrum of specific fragment ions for each peptide.

Data Processing Protocol

Peptide sequences (and hence protein identity) were determined by matching protein databases with the acquired fragmentation pattern by the software program, SEQUEST (ver. 28). (ThermoFisher, San Jose, CA). Enzyme specificity was set to partially tryptic with 2 missed cleavages. Modifications included carboxyamidomethyl (cysteines, fixed) and oxidation (methionine, variable). Mass tolerance was set to 2.0 for precursor ions and 1.0 for fragment ions. The database searched was the Human IPI databases version 3.6. The number of entries in the database was 160,900 which included both the target (forward) and the decoy (reversed) human sequences. Spectral matches were filtered to contain less than 1% FDR at the peptide level based on the target-decoy method. Finally, only tryptic matches were reported and spectral matches were manually examined. When peptides matched to multiple proteins, the peptide was assigned so that only the most logical protein was included (Occam's razor). This same principle was used for isoforms when present in the database.


Xu Li, Experimental Radiation Oncology
Junjie Chen, MD Anderson Cancer Center ( lab head )

Submission Date


Publication Date



    Li X, Tran KM, Aziz KE, Sorokin AV, Chen J, Wang W. Defining the protein-protein interaction network of the human protein tyrosine phosphatase family. Mol Cell Proteomics. 2016 Jul 18. pii: mcp.M116.060277 PubMed: 27432908


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# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 54411 28043 9913 13126 11969 13128 13126
2 54397 28044 10185 13045 12211 13045 13045
3 54410 28045 8867 13825 11449 13827 13825
4 54398 28046 8943 13802 11247 13802 13802
5 54413 28047 9197 14164 11536 14164 14164
6 54412 28289 9508 13591 11703 13591 13591
7 54458 28290 8668 13297 10902 13297 13297
8 54459 28291 8986 13192 11012 13194 13192
9 54399 28292 8498 13368 10660 13371 13368
10 54454 28294 9068 13891 11427 13899 13891